The benthic-index of biotic integrity(B-IBI)was used to evaluate the health status of aquatic ecology in Ji’nan City. Benthic macro-invertebrate assemblages and the aquatic environment were sampled from four ecoregions of 48 sites in the city from May to June, in 2014. Based on multivariate statistical analysis and the principle of least interference, the reference system of B-IBI was built. The B-IBI was developed for river points and reservoir points, respectively. The analyses of the judgment ability and Pearson correlation were conducted on 28 candidate biotic metrics. The core metrics of B-IBI for river points were determined to be four indices: the number of aquatic insect taxa, relative percentage of Crustaceans and Molluscs, BI index, and BWMP index. The metrics of B-IBI for reservoir points included the number of aquatic insect taxa, percentage of advantage number of taxa, and diversity index. The B-IBI values for river and reservoir points, which were transformed into uniform scores by the ratio score method, were obtained. The results show that of the 36 river sampling sites, seven sites were at unhealthy or extremely unhealthy status, 11 sites were at moderately healthy status, eight sites were at sub-healthy status, and three sites were at healthy status. Of the 12 reservoir sampling sites, one site was at healthy status, six sites were at sub-healthy status, four sites were at moderately healthy status, and one site was at extremely unhealthy status. The health status was best in the Yellow River ecoregion and worst in the urban region. The major environmental variables that affected the macro-invertebrate assemblages were the nitrogen content and the percentage of urban construction land.